Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome

Mutations in MECP2 cause Rett syndrome (RTT), an X-linked neurological disorder characterized by regressive loss of neurodevelopmental milestones and acquired psychomotor deficits. However, the cellular heterogeneity of the brain impedes an understanding of how MECP2 mutations contribute to RTT. Here we developed a Cre-inducible method for cell type-specific biotin tagging of MeCP2 in mice. Combining this approach with an allelic series of knockin mice carrying frequent RTT mutations (T158M and R106W) enabled the selective profiling of RTT-associated nuclear transcriptomes in excitatory and inhibitory cortical neurons. We found that most gene expression changes are largely specific to each RTT mutation and cell type. Lowly expressed cell type-enriched genes are preferentially disrupted by MeCP2 mutations, with upregulated and downregulated genes reflecting distinct functional categories. Subcellular RNA analysis in MeCP2 mutant neurons further reveals reductions in the nascent transcription of long genes and uncovers widespread post-transcriptional compensation at the cellular level. Finally, we overcame X-linked cellular mosaicism in female RTT models and identified distinct gene expression changes between neighboring wild-type and mutant neurons, altogether providing contextual insights into RTT etiology that support personalized therapeutic interventions.